Download R 3.5 Mac

06 Dec, 2021 Post a Comment

R 3.5.0 (codename "Joy in Playing") was released yesterday. You can get the latest binaries version from here. (or the .tar.gzsource code from here).

This is a major release with many new features and bug fixes, the full list is provided below.

Upgrading R on Windows and Mac

If you are using Windowsyou can easily upgrade to the latest version of R using the installr package. Simply run the following code in Rgui:

install.packages("installr") # install  setInternet2(TRUE) # only for R versions older than 3.3.0 installr::updateR() # updating R. # If you wish it to go faster, run: installr::updateR(T)

Running "updateR()" will detect if there is a new R version available, and if so it will download+install it (etc.). There is also a step by step tutorial (with screenshots) on how to upgrade R on Windows, using the installr package. If you only see the option to upgrade to an older version of R, then change your mirror or try again in a few hours (it usually take around 24 hours for all CRAN mirrors to get the latest version of R).

If you are using Macyou can easily upgrade to the latest version of R using Andrea Cirillo's updateR package. The package is not on CRAN, so you'll need to run the following code in Rgui:

install.packages("devtools") devtools::install_github("AndreaCirilloAC/updateR") updateR(admin_password = "PASSWORD") # Where "PASSWORD" stands for your system password

Later this year Andrea and I intend to merge the updateR package into installr so that the updateR function will work seamlessly in both Windows and Mac. Stay tuned 🙂

CHANGES IN R 3.5.0

SIGNIFICANT USER-VISIBLE CHANGES

All packages are by default byte-compiled on installation. This makes the installed packages larger (usually marginally so) and may affect the format of messages and tracebacks (which often exclude.Call and similar).

NEW FEATURES

factor() now usesorder() to sort its levels, rather thansort.list(). This allowsfactor() to support custom vector-like objects if methods for the appropriate generics are defined. It has the side effect of makingfactor() succeed on empty or length-one non-atomic vector(-like) types (e.g.,"list"), where it failed before.
diag() gets an optionalnames argument: this may require updates to packages defining S4 methods for it.
chooseCRANmirror() andchooseBioCmirror() no longer have auseHTTPS argument, not needed now allR builds supporthttps:// downloads.
Newsummary() method forwarnings() with a (somewhat experimental)print() method.
(methods package.).self is now automatically registered as a global variable when registering a reference class method.
tempdir(check = TRUE) recreates thetempdir() directory if it is no longer valid (e.g. because some other process has cleaned up the '/tmp' directory).
NewaskYesNo() function and"askYesNo" option to ask the user binary response questions in a customizable but consistent way. (Suggestion of PR#17242.)
New low level utilities...elt(n) and...length() for working with... parts inside a function.

isTRUE() is more tolerant and now true in

                    x <- rlnorm(99)    isTRUE(median(x) == quantile(x)["50%"])

New functionisFALSE() defined analogously toisTRUE().

The default symbol table size has been increased from 4119 to 49157; this may improve the performance of symbol resolution when many packages are loaded. (Suggested by Jim Hester.)
line() gets a new optioniter = 1.
Reading from connections in text mode is buffered, significantly improving the performance ofreadLines(), as well asscan() andread.table(), at least when specifyingcolClasses.
order() is smarter about picking a default sortmethod when its arguments are objects.
available.packages() has two new arguments which control if the values from the per-session repository cache are used (default true, as before) and if so how old cached values can be to be used (default one hour).These arguments can be passed frominstall.packages(),update.packages() and functions calling that: to enable thisavailable.packages(),packageStatus() anddownload.file() gain a... argument.
packageStatus()'supgrade() method no longer ignores its... argument but passes it toinstall.packages().
installed.packages() gains a... argument to allow arguments (includingnoCache) to be passed fromnew.packages(),old.packages(),update.packages() andpackageStatus().
factor(x, levels, labels) now allows duplicatedlabels (not duplicatedlevels!). Hence you can map different values ofx to the same level directly.
Attempting to usenames<-() on an S4 derivative of a basic type no longer emits a warning.
Thelist method ofwithin() gains an optionkeepAttrs = FALSE for some speed-up.
system() andsystem2() now allow the specification of a maximum elapsed time ('timeout').
debug() supports debugging of methods on any object of S4 class"genericFunction", including group generics.
Attempting to increase the length of a variable containingNULL usinglength()<- still has no effect on the target variable, but now triggers a warning.
type.convert() becomes a generic function, with additional methods that operate recursively over list anddata.frame objects. Courtesy of Arni Magnusson (PR#17269).
lower.tri(x) andupper.tri(x) only needingdim(x) now work via new functions.row() and.col(), so no longer callas.matrix() by default in order to work efficiently for all kind of matrix-like objects.
print() methods for"xgettext" and"xngettext" now useencodeString() which keeps, e.g."\n", visible. (Wish of PR#17298.)
package.skeleton() gains an optionalencoding argument.
approx(),spline(),splinefun() andapproxfun() also work for long vectors.
deparse() anddump() are more useful for S4 objects,dput() now using the same internal C code instead of its previous imperfect workaround R code. S4 objects now typically deparse perfectly, i.e., can be recreated identically from deparsed code.dput(),deparse() anddump() now print thenames() information only once, using the more readable(tag = value) syntax, notably forlist()s, i.e., including data frames.
These functions gain a new control option"niceNames" (see.deparseOpts()), which when set (as by default) also uses the(tag = value) syntax for atomic vectors. On the other hand, without deparse options"showAttributes" and"niceNames", names are no longer shown also for lists.as.character(list( c (one = 1))) now includes the name, asas.character(list(list(one = 1))) has always done.

m:n now also deparses nicely whenm > n.

The"quoteExpressions" option, also part of"all", no longerquote()s formulas as that may not re-parse identically. (PR#17378)
If the optionsetWidthOnResize is set andTRUE,R run in a terminal using a recentreadline library will set thewidth option when the terminal is resized. Suggested by Ralf Goertz.
If multipleon.exit() expressions are set usingadd = TRUE then all expressions will now be run even if one signals an error.
mclapply() gets an optionaffinity.list which allows more efficient execution with heterogeneous processors, thanks to Helena Kotthaus.
Thecharacter methods foras.Date() andas.POSIXlt() are more flexiblevia new argumentstryFormats andoptional: see their help pages.
on.exit() gains an optional argumentafter with defaultTRUE. Usingafter = FALSE withadd = TRUE adds an exit expression before any existing ones. This way the expressions are run in a first-in last-out fashion. (From Lionel Henry.)
On Windows,file.rename() internally retries the operation in case of error to attempt to recover from possible anti-virus interference.
Command line completion on:: now also includes lazy-loaded data.
If theTZ environment variable is set when date-time functions are first used, it is recorded as the session default and so will be used rather than the default deduced from the OS ifTZ is subsequently unset.
There is now a[ method for class"DLLInfoList".
glm() andglm.fit get the samesingular.ok = TRUE argument thatlm() has had forever. As a consequence, inglm(*, method = <your_own>), user specified methods need to accept asingular.ok argument as well.
aspell() gains a filter for Markdown ('.md' and '.Rmd') files.
intToUtf8(multiple = FALSE) gains an argument to allow surrogate pairs to be interpreted.
The maximum number of DLLs that can be loaded into R e.g.viadyn.load() has been increased up to 614 when the OS limit on the number of open files allows.
Sys.timezone() on a Unix-alike caches the value at first use in a session:inter alia this means that settingTZ later in the session affects only thecurrent time zone and not thesystem one.Sys.timezone() is now used to find the system timezone to pass to the code used whenR is configured with–with-internal-tzcode.
Whentar() is used with an external command which is detected to be GNUtar or libarchivetar (akabsdtar), a different command-line is generated to circumvent line-length limits in the shell.
system(*, intern = FALSE),system2() (when not capturing output),file.edit() andfile.show() now issue a warning when the external command cannot be executed.
The "default" ("lm" etc) methods ofvcov() have gained new optional argumentcomplete = TRUE which makes thevcov() methods more consistent with thecoef()methods in the case of singular designs. The former (back-compatible) behavior is given byvcov(*, complete = FALSE).
coef() methods (forlm etc) also gain acomplete = TRUE optional argument for consistency withvcov().
For"aov", bothcoef() andvcov() methods remain back-compatibly consistent, using theother default,complete = FALSE.
attach(*, pos = 1) is now an error instead of a warning.
New functiongetDefaultCluster() in packageparallel to get the default cluster set viasetDefaultCluster().
str(x) for atomic objectsx now treats both cases ofis.vector(x) similarly, and hence much less often prints"atomic". This is a slight non-back-compatible change producing typically both more informative and shorter output.
write.dcf() gets optional argumentuseBytes.
New, partly experimentalpackageDate() which tries to get a valid"Date" object from a package 'DESCRIPTION' file, thanks to suggestions in PR#17324.
tools::resaveRdaFiles() gains aversion argument, for use when packages should remain compatible with earlier versions ofR.
ar.yw(x) and hence by defaultar(x) now work whenx hasNAs, mostly thanks to a patch by Pavel Krivitsky in PR#17366. Thear.yw.default()'s AIC computations have become more efficient by usingdeterminant().
NewwarnErrList() utility (from packagenlme, improved).
By default the (arbitrary) signs of the loadings fromprincomp() are chosen so the first element is non-negative.
If–default-packages is not used, thenRscript now checks the environment variableR_SCRIPT_DEFAULT_PACKAGES. If this is set, then it takes precedence overR_DEFAULT_PACKAGES. If default packages are not specified on the command line or by one of these environment variables, thenRscript now uses the same default packages asR. For now, the previous behavior of not includingmethods can be restored by setting the environment variableR_SCRIPT_LEGACY toyes.
When a package is found more than once, the warning fromfind.package(*, verbose=TRUE) lists all library locations.
POSIXt objects can now also be rounded or truncated to month or year.
stopifnot() can be used alternatively via new argumentexprs which is nicer and useful when testing several expressions in one call.
The environment variableR_MAX_VSIZE can now be used to specify the maximal vector heap size. On macOS, unless specified by this environment variable, the maximal vector heap size is set to the maximum of 16GB and the available physical memory. This is to avoid having theR process killed when macOS over-commits memory.
sum(x) andsum(x1,x2,..,x<N>) with many or long logical or integer vectors no longer overflows (and returnsNA with a warning), but returnsdouble numbers in such cases.
Single components of"POSIXlt" objects can now be extracted and replaced via[ indexing with 2 indices.
S3 method lookup now searches the namespace registry after the top level environment of the calling environment.
Arithmetic sequences created by1:n,seq_along, and the like now use compact internal representations via theALTREP framework. Coercing integer and numeric vectors to character also now uses theALTREP framework to defer the actual conversion until first use.
Finalizers are now run with interrupts suspended.
merge() gains new optionno.dups and by default suffixes the second of two duplicated column names, thanks to a proposal by Scott Ritchie (and Gabe Becker).
scale.default(x, center, scale) now also allowscenter orscale to be "numeric-alike", i.e., such thatas.numeric(.) coerces them correctly. This also eliminates a wrong error message in such cases.
par*apply andpar*applyLB gain an optional argumentchunk.size which allows to specify the granularity of scheduling.
Someas.data.frame() methods, notably thematrix one, are now more careful in not accepting duplicated orNA row names, and by default produce unique non-NA row names. This is based on new function.rowNamesDF(x, make.names = *) <- rNms where the logical argumentmake.names allows to specifyhow invalid row namesrNms are handled..rowNamesDF() is a "workaround" compatible default.
R has new serialization format (version 3) which supports custom serialization ofALTREP framework objects. These objects can still be serialized in format 2, but less efficiently. Serialization format 3 also records the current native encoding of unflagged strings and converts them when de-serialized in R running under different native encoding. Format 3 comes with new serialization magic numbers (RDA3, RDB3, RDX3). Format 3 can be selected byversion = 3 insave(),serialize() andsaveRDS(), but format 2 remains the default for all serialization and saving of the workspace. Serialized data in format 3 cannot be read by versions ofR prior to version 3.5.0.
The"Date" and "date-time" classes"POSIXlt" and"POSIXct" now have a working`length<-` method, as wished in PR#17387.
optim(*, control = list(warn.1d.NelderMead = FALSE)) allows to turn off the warning when applying the default"Nelder-Mead" method to 1-dimensional problems.
matplot(.., panel.first = .) etc now work, aslog becomes explicit argument and... is passed toplot() unevaluated, as suggested by Sebastian Meyer in PR#17386.
Interrupts can be suspended while evaluating an expression usingsuspendInterrupts. Subexpression can be evaluated with interrupts enabled usingallowInterrupts. These functions can be used to make sure cleanup handlers cannot be interrupted.
R 3.5.0 includes a framework that allows packages to provide alternate representations of basicR objects (ALTREP). The framework is still experimental and may undergo changes in futureR releases as more experience is gained. For now, documentation is provided in https://svn.r-project.org/R/branches/ALTREP/ALTREP.html.

UTILITIES

install.packages() for source packages now has the possibility to set a 'timeout' (elapsed-time limit). For serial installs this uses thetimeout argument ofsystem2(): for parallel installs it requires thetimeout utility command from GNUcoreutils.
It is now possible to set 'timeouts' (elapsed-time limits) for most parts ofR CMD checkvia environment variables documented in the 'R Internals' manual.
The 'BioC extra' repository which was dropped from Bioconductor 3.6 and later has been removed fromsetRepositories(). This changes the mapping for 6–8 used bysetRepositories(ind=).
R CMD check now also applies the settings of environment variables_R_CHECK_SUGGESTS_ONLY_ and_R_CHECK_DEPENDS_ONLY_ to the re-building of vignettes.
R CMD check with environment variable_R_CHECK_DEPENDS_ONLY_ set to a true value makes test-suite-management packages available and (for the time being) works around a common omission ofrmarkdown from theVignetteBuilder field.

INSTALLATION on a UNIX-ALIKE

Support for a system Java on macOS has been removed — install a fairly recent Oracle Java (see 'R Installation and Administration' §C.3.2).
configure works harder to set additional flags inSAFE_FFLAGS only where necessary, and to use flags which have little or no effect on performance.In rare circumstances it may be necessary to override the setting ofSAFE_FFLAGS.
C99 functionsexpm1,hypot,log1p andnearbyint are now required.
configure sets a-std flag for the C++ compiler for all supported C++ standards (e.g.,-std=gnu++11 for the C++11 compiler). Previously this was not done in a few cases where the default standard passed the tests made (e.g.clang 6.0.0 for C++11).

C-LEVEL FACILITIES

'Writing R Extensions' documents macrosMAYBE_REFERENCED,MAYBE_SHARED andMARK_NOT_MUTABLE that should be used by packageC code insteadNAMED orSET_NAMED.
The object header layout has been changed to support merging theALTREP branch. This requires re-installing packages that use compiled code.
'Writing R Extensions' now documents theR_tryCatch,R_tryCatchError, andR_UnwindProtect functions.
NAMEDMAX has been raised to 3 to allow protection of intermediate results from (usually ill-advised) assignments in arguments toBUILTIN functions. PackageC code usingSET_NAMED may need to be revised.

DEPRECATED AND DEFUNCT

Sys.timezone(location = FALSE) is defunct, and is ignored (with a warning).
methods:::bind_activation() is defunct now; it typically has been unneeded for years.The undocumented 'hidden' objects.__H__.cbind and.__H__.rbind in packagebase are deprecated (in favour ofcbind andrbind).
The declaration ofpythag() in 'Rmath.h' has been removed — the entry point has not been provided sinceR 2.14.0.

BUG FIXES

printCoefmat() now also works without column names.
The S4 methods onOps() for the"structure" class no longer cause infinite recursion when the structure is not an S4 object.
nlm(f, ..) for the case wheref() has a"hessian" attribute now computesLL' = H + µI correctly. (PR#17249).
An S4 method that "rematches" to its generic and overrides the default value of a generic formal argument toNULL no longer drops the argument from its formals.
Rscript can now accept more than one argument given on the#! line of a script. Previously, one could only pass a single argument on the#! line in Linux.
Connections are now written correctly with encoding"UTF-16LE". (PR#16737).
Evaluation of..0 now signals an error. When..1 is used and... is empty, the error message is more appropriate.
(Windows mainly.) Unicode code points which require surrogate pairs in UTF-16 are now handled. All systems should properly handle surrogate pairs, even those systems that do not need to make use of them. (PR#16098)
stopifnot(e, e2, ...) now evaluates the expressions sequentially and in case of an error or warning shows the relevant expression instead of the fullstopifnot(..) call.
path.expand() on Windows now accepts paths specified as UTF-8-encoded character strings even if not representable in the current locale. (PR#17120)
line(x, y) now correctly computes the medians of the left and right group's x-values and in all cases reproduces straight lines.
Extending S4 classes with slots corresponding to special attributes likedim anddimnames now works.
Fix forlegend() whenfill has multiple values the first of which isNA (all colours used to default topar(fg)). (PR#17288)
installed.packages() did not remove the cached value for a library tree that had been emptied (but would not use the old value, just waste time checking it).
The documentation forinstalled.packages(noCache = TRUE) incorrectly claimed it would refresh the cache.
aggregate(<data.frame>) no longer uses spurious names in some cases. (PR#17283)
object.size() now also works for long vectors.
packageDescription() tries harder to solve re-encoding issues, notably seen in some Windows locales. This fixes thecitation() issue in PR#17291.
poly(<matrix>, 3) now works, thanks to prompting by Marc Schwartz.
readLines() no longer segfaults on very large files with embedded'\0' (aka 'nul') characters. (PR#17311)
ns() (packagesplines) now also works for a single observation.interpSpline() gives a more friendly error message when the number of points is less than four.
dist(x, method = "canberra") now uses the correct definition; the result may only differ whenx contains values of differing signs, e.g. not for 0-1 data.
methods:::cbind() andmethods:::rbind() avoid deep recursion, thanks to Suharto Anggono via PR#17300.
Arithmetic with zero-column data frames now works more consistently; issue raised by Bill Dunlap.Arithmetic with data frames gives a data frame for^ (which previously gave a numeric matrix).
pretty(x, n) for largen or largediff(range(x)) now works better (though it was never meant for largen); internally it uses the same rounding fuzz (1e-10) asseq.default() — as it did up to 2010-02-03 when both were 1e-7.
Internal C-levelR_check_class_and_super() and henceR_check_class_etc() now also consider non-direct super classes and hence return a match in more cases. This e.g., fixes behaviour of derived classes in packageMatrix.
Reverted unintended change in behavior ofreturn calls inon.exit expressions introduced by stack unwinding changes inR 3.3.0.
Attributes on symbols are now detected and prevented; attempt to add an attribute to a symbol results in an error.
fisher.test(*, workspace = <n>) now may also increase the internal stack size which allows larger problem to be solved, fixing PR#1662.
Themethods package no longer directly copies slots (attributes) into a prototype that is of an "abnormal" (reference) type, like a symbol.
Themethods package no longer attempts to calllength<-() onNULL (during the bootstrap process).
Themethods package correctly shows methods when there are multiple methods with the same signature for the same generic (still not fully supported, but at least the user can see them).
sys.on.exit() is now always evaluated in the right frame. (From Lionel Henry.)
seq.POSIXt(*, by = "<n> DSTdays") now should work correctly in all cases and is faster. (PR#17342)
.C() when returning a logical vector now always maps values other than FALSE and NA to TRUE (as documented).
Subassignment with zero length vectors now coerces as documented (PR#17344).
Further,x <- numeric(); x[1] <- character() now signals an error 'replacement has length zero' (or a translation of that) instead of doing nothing.
(Packageparallel.)mclapply(),pvec() andmcparallel() (whenmccollect() is used to collect results) no longer leave zombie processes behind.
R CMD INSTALL <pkg> now produces the intended error message when, e.g., theLazyData field is invalid.
as.matrix(dd) now works when the data framedd contains a column which is a data frame or matrix, including a 0-column matrix/d.f. .
mclapply(X, mc.cores) now follows its documentation and callslapply() in casemc.cores = 1 also in the casemc.preschedule is false. (PR#17373)
aggregate(<data.frame>, drop=FALSE) no longer calls the function on <empty> parts but sets corresponding results toNA. (Thanks to Suharto Anggono's patches in PR#17280).
Theduplicated() method for data frames is now based on thelist method (instead of string coercion). Consequentlyunique() is better distinguishing data frame rows, fixing PR#17369 and PR#17381. The methods for matrices and arrays are changed accordingly.
Callingnames() on an S4 object derived from"environment" behaves (by default) like callingnames() on an ordinary environment.
read.table() with a non-default separator now supports quotes following a non-whitespace character, matching the behavior ofscan().
parLapplyLB andparSapplyLB have been fixed to do load balancing (dynamic scheduling). This also means that results of computations depending on random number generators will now really be non-reproducible, as documented.
Indexing a list using dollar and empty string (l$"") returns NULL.
Using\usage{ data(<name>, package="<pkg>") }no longer producesR CMD check warnings.
match.arg() more carefully chooses the environment for constructing defaultchoices, fixing PR#17401 as proposed by Duncan Murdoch.
Deparsing of consecutive! calls is now consistent with deparsing unary- and+ calls and creates code that can be reparsed exactly; thanks to a patch by Lionel Henry inPR#17397. (As a side effect, this uses fewer parentheses in some other deparsing involving! calls.)